There is already a description here of how to do stratified train/test split in scikit via train_test_split (Stratified Train/Test-split in scikit-learn) and a description of ho
The solution is to just use StratifiedShuffleSplit twice, like below:
from sklearn.model_selection import StratifiedShuffleSplit
split = StratifiedShuffleSplit(n_splits=1, test_size=0.4, random_state=42)
for train_index, test_valid_index in split.split(df, df.target):
train_set = df.iloc[train_index]
test_valid_set = df.iloc[test_valid_index]
split2 = StratifiedShuffleSplit(n_splits=1, test_size=0.5, random_state=42)
for test_index, valid_index in split2.split(test_valid_set, test_valid_set.target):
test_set = test_valid_set.iloc[test_index]
valid_set = test_valid_set.iloc[valid_index]